SYNOPSIS

perl asarp.pl output_file config_file [optional: parameter_file]

NEW: the ASARP pipeline now supports strand-specific RNA-Seq data (which can be processed by the new pre-processing script: procReads. One can set the optional strand-specific flag in the cnofig file. IMPORTANT: the strand-specific option does not work correctly on non-strand-specific data.

ARGUMENTS:

config_file the input configuration file which contains all the input file keys and their paths

OPTIONAL:

parameter_file the parameter configuration file which contains all the thresholds and cutoffs
if not input, the default.param file in the ASARP main program directory will be used

Details of the input config and parameter files can be found in the Files page. For preparation of the input files used in config_file, see the pre-processing section: rmDup, mergeSam, procReads

OUTPUTS

output_file is where the ASARP result summary is output, and meanwhile there will be 4 addtional detailed result files output:

output_file.ase.prediction
-- the detailed results of (whole-gene-level) ASE patterns (exclusive to other ASARP patterns: AI, AS or AT)

How to categorize ASARP patterns into specific Allele-Specific AI/AS/AT and/or combinations of them depends on whether the candidate SNV locations are in internal exons/introns (AS) and/or alternative 3' or 5' UTRs (AI/AT). A complex ASARP gene is with ASARP SNVs in more than one categories.

NEV: Normalized Expression Value, a PSI (Percent Spliced-In) like value to measure whether an event (also alternatively processed region) is also alternatively processed according to RNA-Seq (gene expression). It is calculated as (note that in some events only NEV_gene is available)